1
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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2
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Nishida N, Ito Y, Shimada I. In situ structural biology using in-cell NMR. Biochim Biophys Acta Gen Subj 2019; 1864:129364. [PMID: 31103749 DOI: 10.1016/j.bbagen.2019.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 01/23/2023]
Abstract
BACKGROUND Accumulating evidence from the experimental and computational studies indicated that the functional properties of proteins are different between in vitro and living cells, raising the necessity to examine the protein structure under the native intracellular milieu. To gain structural information of the proteins inside the living cells at an atomic resolution, in-cell NMR method has been developed for the past two decades. SCOPE OF REVIEW In this review, we will overview the recent progress in the methodological developments and the biological applications of in-cell NMR, and discuss the advances and challenges in this filed. MAJOR CONCLUSIONS A number of methods were developed to enrich the isotope-labeled proteins inside the cells, enabling the in-cell NMR observation of bacterial cells as well as eukaryotic cells. In-cell NMR has been applied to various biological systems, including de novo structure determinations, protein/protein or protein/drug interactions, and monitoring of chemical reactions exerted by the endogenous enzymes. The bioreactor system, in which the cells in the NMR tube are perfused by fresh culture medium, enabled the long-term in-cell NMR measurements, and the real-time observations of intracellular responses upon external stimuli. GENERAL SIGNIFICANCE In-cell NMR has become a unique technology for its ability to obtain the function-related structural information of the target proteins under the physiological or pathological cellular environments, which cannot be reconstituted in vitro.
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Affiliation(s)
- Noritaka Nishida
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan.
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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3
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Reardon PN, Walter ED, Marean-Reardon CL, Lawrence CW, Kleber M, Washton NM. Carbohydrates protect protein against abiotic fragmentation by soil minerals. Sci Rep 2018; 8:813. [PMID: 29339803 PMCID: PMC5770415 DOI: 10.1038/s41598-017-19119-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/21/2017] [Indexed: 11/10/2022] Open
Abstract
The degradation and turnover of soil organic matter is an important part of global carbon cycling and of particular importance with respect to attempts to predict the response of ecosystems to global climate change. Thus, it is important to mechanistically understand the processes by which organic matter can be degraded in the soil environment, including contact with reactive or catalytic mineral surfaces. We have characterized the outcome of the interaction of two minerals, birnessite and kaolinite, with two disaccharides, cellobiose and trehalose. These results show that birnessite reacts with and degrades the carbohydrates, while kaolinite does not. The reaction of disaccharides with birnessite produces Mn(II), indicating that degradation of the disaccharides is the result of their oxidation by birnessite. Furthermore, we find that both sugars can inhibit the degradation of a model protein by birnessite, demonstrating that the presence of one organic constituent can impact abiotic degradation of another. Therefore, both the reactivity of the mineral matrix and the presence of certain organic constituents influence the outcomes of abiotic degradation. These results suggest the possibility that microorganisms may be able to control the functionality of exoenzymes through the concomitant excretion of protective organic substances, such as those found in biofilms.
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Affiliation(s)
- Patrick N Reardon
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA. .,OSU NMR Facility, Oregon State University, Corvallis, OR, 97331, USA.
| | - Eric D Walter
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Carrie L Marean-Reardon
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.,School of the Environment, Washington State University Tri-Cities, Richland, WA, 99352, USA
| | - Chad W Lawrence
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Markus Kleber
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Nancy M Washton
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
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4
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Lippens G, Cahoreau E, Millard P, Charlier C, Lopez J, Hanoulle X, Portais JC. In-cell NMR: from metabolites to macromolecules. Analyst 2018; 143:620-629. [PMID: 29333554 DOI: 10.1039/c7an01635b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In-cell NMR of macromolecules has gained momentum over the last ten years as an approach that might bridge the branches of cell biology and structural biology. In this review, we put it in the context of earlier efforts that aimed to characterize by NMR the cellular environment of live cells and their intracellular metabolites. Although technical aspects distinguish these earlier in vivo NMR studies and the more recent in cell NMR efforts to characterize macromolecules in a cellular environment, we believe that both share major concerns ranging from sensitivity and line broadening to cell viability. Approaches to overcome the limitations in one subfield thereby can serve the other one and vice versa. The relevance in biomedical sciences might stretch from the direct following of drug metabolism in the cell to the observation of target binding, and thereby encompasses in-cell NMR both of metabolites and macromolecules. We underline the efforts of the field to move to novel biological insights by some selected examples.
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Affiliation(s)
- G Lippens
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - E Cahoreau
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - P Millard
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - C Charlier
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - J Lopez
- CERMN, Seccion Quimica, Departemento de Ciencias, Pontificia Universidad Catolica del Peru, Lima 32, Peru
| | - X Hanoulle
- Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), University of Lille, CNRS UMR8576, Lille, France
| | - J C Portais
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
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5
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Cohen RD, Pielak GJ. Quinary interactions with an unfolded state ensemble. Protein Sci 2017; 26:1698-1703. [PMID: 28571108 PMCID: PMC5563149 DOI: 10.1002/pro.3206] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 05/21/2017] [Accepted: 05/26/2017] [Indexed: 01/10/2023]
Abstract
Anfinsen's thermodynamic hypothesis states that the native three-dimensional fold of a protein represents the structure with the lowest Gibbs free energy. Changes in the free energy of denaturation can arise from changes to the folded state, the unfolded state, or both. It has been recently recognized that quinary interactions, transient contacts that take place only in cells, can modulate protein stability through interactions involving the folded state. Here we show that the cellular environment can also remodel the unfolded state ensemble.
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Affiliation(s)
- Rachel D. Cohen
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599
| | - Gary J. Pielak
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599
- Department of Biochemistry and BiophysicsUniversity of North CarolinaChapel HillNorth Carolina27599
- Lineberger Comprehensive Cancer Center, University of North CarolinaChapel HillNorth Carolina27599
- Integrative Program for Biological and Genome SciencesUniversity of North CarolinaChapel HillNorth Carolina27599
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6
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Towards understanding cellular structure biology: In-cell NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:547-557. [PMID: 28257994 DOI: 10.1016/j.bbapap.2017.02.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/22/2017] [Accepted: 02/27/2017] [Indexed: 12/20/2022]
Abstract
To watch biological macromolecules perform their functions inside the living cells is the dream of any biologists. In-cell nuclear magnetic resonance is a branch of biomolecular NMR spectroscopy that can be used to observe the structures, interactions and dynamics of these molecules in the living cells at atomic level. In principle, in-cell NMR can be applied to different cellular systems to achieve biologically relevant structural and functional information. In this review, we summarize the existing approaches in this field and discuss its applications in protein interactions, folding, stability and post-translational modifications. We hope this review will emphasize the effectiveness of in-cell NMR for studies of intricate biological processes and for structural analysis in cellular environments.
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7
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Pastore A, Temussi PA. The Emperor's new clothes: Myths and truths of in-cell NMR. Arch Biochem Biophys 2017; 628:114-122. [PMID: 28259514 DOI: 10.1016/j.abb.2017.02.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 02/24/2017] [Accepted: 02/27/2017] [Indexed: 11/25/2022]
Abstract
In-cell NMR is a technique developed to study the structure and dynamical behavior of biological macromolecules in their natural environment, circumventing all isolation and purification steps. In principle, the potentialities of the technique are enormous, not only for the possibility of bypassing all purification steps but, even more importantly, for the wealth of information that can be gained from directly monitoring interactions among biological macromolecules in a natural cell. Here, we review critically the promises, successes and limits of this technique as it stands now. Interestingly, many of the problems of NMR in bacterial cells stem from the artificially high concentration of the protein under study whose overexpression is anyway necessary to select it from the background. This has, as a consequence, that when overexpressed, most globular proteins, do not show an NMR spectrum, limiting the applicability of the technique to intrinsically unfolded or specifically behaving proteins. The outlook for in-cell NMR of eukaryotic cells is more promising and is possibly the most attracting aspect for the future.
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Affiliation(s)
- Annalisa Pastore
- The Wohl Institute, King's College London, 5 Cutcombe Rd, London SE5 9RT, UK; University of Pavia, Department of Molecular Medicine, Pavia, Italy.
| | - Piero Andrea Temussi
- The Wohl Institute, King's College London, 5 Cutcombe Rd, London SE5 9RT, UK; University of Naples "Federico II", Department of Chemical Sciences, Naples, Italy
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8
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Cohen RD, Pielak GJ. A cell is more than the sum of its (dilute) parts: A brief history of quinary structure. Protein Sci 2017; 26:403-413. [PMID: 27977883 PMCID: PMC5326556 DOI: 10.1002/pro.3092] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/02/2016] [Accepted: 12/02/2016] [Indexed: 01/01/2023]
Abstract
Most knowledge of protein structure and function is derived from experiments performed with purified protein resuspended in dilute, buffered solutions. However, proteins function in the crowded, complex cellular environment. Although the first four levels of protein structure provide important information, a complete understanding requires consideration of quinary structure. Quinary structure comprises the transient interactions between macromolecules that provides organization and compartmentalization inside cells. We review the history of quinary structure in the context of several metabolic pathways, and the technological advances that have yielded recent insight into protein behavior in living cells. The evidence demonstrates that protein behavior in isolated solutions deviates from behavior in the physiological environment.
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Affiliation(s)
- Rachel D. Cohen
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599
| | - Gary J. Pielak
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599
- Department of Biochemistry and BiophysicsUniversity of North CarolinaChapel HillNorth Carolina27599
- Lineberger Comprehensive Cancer Center, University of North CarolinaChapel HillNorth Carolina27599
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9
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Reardon PN, Chacon SS, Walter ED, Bowden ME, Washton NM, Kleber M. Abiotic Protein Fragmentation by Manganese Oxide: Implications for a Mechanism to Supply Soil Biota with Oligopeptides. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:3486-3493. [PMID: 26974439 DOI: 10.1021/acs.est.5b04622] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The ability of plants and microorganisms to take up organic nitrogen in the form of free amino acids and oligopeptides has received increasing attention over the last two decades, yet the mechanisms for the formation of such compounds in soil environments remain poorly understood. We used Nuclear Magnetic Resonance (NMR) and Electron Paramagnetic Resonance (EPR) spectroscopies to distinguish the reaction of a model protein with a pedogenic oxide (Birnessite, MnO2) from its response to a phyllosilicate (Kaolinite). Our data demonstrate that birnessite fragments the model protein while kaolinite does not, resulting in soluble peptides that would be available to soil biota and confirming the existence of an abiotic pathway for the formation of organic nitrogen compounds for direct uptake by plants and microorganisms. The absence of reduced Mn(II) in the solution suggests that birnessite acts as a catalyst rather than an oxidant in this reaction. NMR and EPR spectroscopies are shown to be valuable tools to observe these reactions and capture the extent of protein transformation together with the extent of mineral response.
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Affiliation(s)
- Patrick N Reardon
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory , Richland, Washington 99354, United States
| | - Stephany S Chacon
- Department of Crop and Soil Science, Oregon State University , Corvallis, Oregon 97331, United States
| | - Eric D Walter
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory , Richland, Washington 99354, United States
| | - Mark E Bowden
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory , Richland, Washington 99354, United States
| | - Nancy M Washton
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory , Richland, Washington 99354, United States
| | - Markus Kleber
- Department of Crop and Soil Science, Oregon State University , Corvallis, Oregon 97331, United States
- Institut für Bodenlandschaftsforschung, Leibniz Zentrum für Agrarlandschaftsforschung (ZALF) , Eberswalder Straße 84, 15374 Müncheberg, Germany
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10
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Reardon PN, Marean-Reardon CL, Bukovec MA, Coggins BE, Isern NG. 3D TOCSY-HSQC NMR for Metabolic Flux Analysis Using Non-Uniform Sampling. Anal Chem 2016; 88:2825-31. [PMID: 26849182 DOI: 10.1021/acs.analchem.5b04535] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
(13)C-Metabolic Flux Analysis ((13)C-MFA) is rapidly being recognized as the authoritative method for determining fluxes through metabolic networks. Site-specific (13)C enrichment information obtained using NMR spectroscopy is a valuable input for (13)C-MFA experiments. Chemical shift overlaps in the 1D or 2D NMR experiments typically used for (13)C-MFA frequently hinder assignment and quantitation of site-specific (13)C enrichment. Here we propose the use of a 3D TOCSY-HSQC experiment for (13)C-MFA. We employ Non-Uniform Sampling (NUS) to reduce the acquisition time of the experiment to a few hours, making it practical for use in (13)C-MFA experiments. Our data show that the NUS experiment is linear and quantitative. Identification of metabolites in complex mixtures, such as a biomass hydrolysate, is simplified by virtue of the (13)C chemical shift obtained in the experiment. In addition, the experiment reports (13)C-labeling information that reveals the position specific labeling of subsets of isotopomers. The information provided by this technique will enable more accurate estimation of metabolic fluxes in large metabolic networks.
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Affiliation(s)
- P N Reardon
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , 3335 Innovation Boulevard, Richland, Washington 99352, United States
| | - C L Marean-Reardon
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , 3335 Innovation Boulevard, Richland, Washington 99352, United States.,Department of Environmental Sciences, Washington State University , Richland, Washington 99354, United States
| | - M A Bukovec
- Department of Chemical, Paper and Biomedical Engineering, Miami University , Oxford, Ohio 45056, United States
| | - B E Coggins
- Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - N G Isern
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , 3335 Innovation Boulevard, Richland, Washington 99352, United States
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11
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Abstract
Conventional structural and chemical biology approaches are applied to macromolecules extrapolated from their native context. When this is done, important structural and functional features of macromolecules, which depend on their native network of interactions within the cell, may be lost. In-cell nuclear magnetic resonance is a branch of biomolecular NMR spectroscopy that allows macromolecules to be analyzed in living cells, at the atomic level. In-cell NMR can be applied to several cellular systems to obtain biologically relevant structural and functional information. Here we summarize the existing approaches and focus on the applications to protein folding, interactions, and post-translational modifications.
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Affiliation(s)
- Enrico Luchinat
- From the Magnetic Resonance Center (CERM), the Department of Biomedical, Clinical and Experimental Sciences, and
| | - Lucia Banci
- From the Magnetic Resonance Center (CERM), the Department of Chemistry, University of Florence, Florence 50121, Italy
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12
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Cohen RD, Guseman AJ, Pielak GJ. Intracellular pH modulates quinary structure. Protein Sci 2015; 24:1748-55. [PMID: 26257390 DOI: 10.1002/pro.2765] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 08/03/2015] [Indexed: 12/19/2022]
Abstract
NMR spectroscopy can provide information about proteins in living cells. pH is an important characteristic of the intracellular environment because it modulates key protein properties such as net charge and stability. Here, we show that pH modulates quinary interactions, the weak, ubiquitous interactions between proteins and other cellular macromolecules. We use the K10H variant of the B domain of protein G (GB1, 6.2 kDa) as a pH reporter in Escherichia coli cells. By controlling the intracellular pH, we show that quinary interactions influence the quality of in-cell (15) N-(1) H HSQC NMR spectra. At low pH, the quality is degraded because the increase in attractive interactions between E. coli proteins and GB1 slows GB1 tumbling and broadens its crosspeaks. The results demonstrate the importance of quinary interactions for furthering our understanding of protein chemistry in living cells.
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Affiliation(s)
- Rachel D Cohen
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, 27599
| | - Alex J Guseman
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, 27599
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, 27599.,Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, 27599
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13
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Popovic M, Sanfelice D, Pastore C, Prischi F, Temussi PA, Pastore A. Selective observation of the disordered import signal of a globular protein by in-cell NMR: the example of frataxins. Protein Sci 2015; 24:996-1003. [PMID: 25772583 PMCID: PMC4456112 DOI: 10.1002/pro.2679] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/08/2015] [Indexed: 01/16/2023]
Abstract
We have exploited the capability of in-cell NMR to selectively observe flexible regions within folded proteins to carry out a comparative study of two members of the highly conserved frataxin family which are found both in prokaryotes and in eukaryotes. They all contain a globular domain which shares more than 50% identity, which in eukaryotes is preceded by an N-terminal tail containing the mitochondrial import signal. We demonstrate that the NMR spectrum of the bacterial ortholog CyaY cannot be observed in the homologous E. coli system, although it becomes fully observable as soon as the cells are lysed. This behavior has been observed for several other compact globular proteins as seems to be the rule rather than the exception. The NMR spectrum of the yeast ortholog Yfh1 contains instead visible signals from the protein. We demonstrate that they correspond to the flexible N-terminal tail indicating that this is flexible and unfolded. This flexibility of the N-terminus agrees with previous studies of human frataxin, despite the extensive sequence diversity of this region in the two proteins. Interestingly, the residues that we observe in in-cell experiments are not visible in the crystal structure of a Yfh1 mutant designed to destabilize the first helix. More importantly, our results show that, in cell, the protein is predominantly present not as an aggregate but as a monomeric species.
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Affiliation(s)
- Matija Popovic
- National Institute for Medical Research, MRC, The RidgewayLondon, United Kingdom
| | - Domenico Sanfelice
- Department of Clinical Neuroscience, King's College London, Denmark Hill CampusLondon, United Kingdom
| | - Chiara Pastore
- Department of Life Sciences, Centre for Structural Biology, Sir Ernst Chain Building, Imperial College LondonLondon, SW7 2AZ, United Kingdom
| | - Filippo Prischi
- Department of Life Sciences, Centre for Structural Biology, Sir Ernst Chain Building, Imperial College LondonLondon, SW7 2AZ, United Kingdom
| | - Piero Andrea Temussi
- National Institute for Medical Research, MRC, The RidgewayLondon, United Kingdom
| | - Annalisa Pastore
- Department of Clinical Neuroscience, King's College London, Denmark Hill CampusLondon, United Kingdom
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14
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Kyne C, Ruhle B, Gautier VW, Crowley PB. Specific ion effects on macromolecular interactions in Escherichia coli extracts. Protein Sci 2014; 24:310-8. [PMID: 25492389 DOI: 10.1002/pro.2615] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 11/25/2014] [Accepted: 11/27/2014] [Indexed: 12/16/2022]
Abstract
Protein characterization in situ remains a major challenge for protein science. Here, the interactions of ΔTat-GB1 in Escherichia coli cell extracts were investigated by NMR spectroscopy and size exclusion chromatography (SEC). ΔTat-GB1 was found to participate in high molecular weight complexes that remain intact at physiologically-relevant ionic strength. This observation helps to explain why ΔTat-GB1 was not detected by in-cell NMR spectroscopy. Extracts pre-treated with RNase A had a different SEC elution profile indicating that ΔTat-GB1 predominantly interacted with RNA. The roles of biological and laboratory ions in mediating macromolecular interactions were studied. Interestingly, the interactions of ΔTat-GB1 could be disrupted by biologically-relevant multivalent ions. The most effective shielding of interactions occurred in Mg(2+) -containing buffers. Moreover, a combination of RNA digestion and Mg(2+) greatly enhanced the NMR detection of ΔTat-GB1 in cell extracts.
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Affiliation(s)
- Ciara Kyne
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
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15
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Smith AE, Zhang Z, Pielak GJ, Li C. NMR studies of protein folding and binding in cells and cell-like environments. Curr Opin Struct Biol 2014; 30:7-16. [PMID: 25479354 DOI: 10.1016/j.sbi.2014.10.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 10/20/2014] [Accepted: 10/24/2014] [Indexed: 11/18/2022]
Abstract
Proteins function in cells where the concentration of macromolecules can exceed 300g/L. The ways in which this crowded environment affects the physical properties of proteins remain poorly understood. We summarize recent NMR-based studies of protein folding and binding conducted in cells and in vitro under crowded conditions. Many of the observations can be understood in terms of interactions between proteins and the rest of the intracellular environment (i.e. quinary interactions). Nevertheless, NMR studies of folding and binding in cells and cell-like environments remain in their infancy. The frontier involves investigations of larger proteins and further efforts in higher eukaryotic cells.
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Affiliation(s)
- Austin E Smith
- Department of Chemistry, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599-3290, USA
| | - Zeting Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599-3290, USA; Department of Biochemistry and Biophysics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599-3290, USA.
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China.
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16
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Abstract
The intracellular milieu differs from the dilute conditions in which most biophysical and biochemical studies are performed. This difference has led both experimentalists and theoreticians to tackle the challenging task of understanding how the intracellular environment affects the properties of biopolymers. Despite a growing number of in-cell studies, there is a lack of quantitative, residue-level information about equilibrium thermodynamic protein stability under nonperturbing conditions. We report the use of NMR-detected hydrogen-deuterium exchange of quenched cell lysates to measure individual opening free energies of the 56-aa B1 domain of protein G (GB1) in living Escherichia coli cells without adding destabilizing cosolutes or heat. Comparisons to dilute solution data (pH 7.6 and 37 °C) show that opening free energies increase by as much as 1.14 ± 0.05 kcal/mol in cells. Importantly, we also show that homogeneous protein crowders destabilize GB1, highlighting the challenge of recreating the cellular interior. We discuss our findings in terms of hard-core excluded volume effects, charge-charge GB1-crowder interactions, and other factors. The quenched lysate method identifies the residues most important for folding GB1 in cells, and should prove useful for quantifying the stability of other globular proteins in cells to gain a more complete understanding of the effects of the intracellular environment on protein chemistry.
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Abstract
Inside cells, the concentration of macromolecules can reach up to 400 g/L. In such crowded environments, proteins are expected to behave differently than in vitro. It has been shown that the stability and the folding rate of a globular protein can be altered by the excluded volume effect produced by a high density of macromolecules. However, macromolecular crowding effects on intrinsically disordered proteins (IDPs) are less explored. These proteins can be extremely dynamic and potentially sample a wide ensemble of conformations under non-denaturing conditions. The dynamic properties of IDPs are intimately related to the timescale of conformational exchange within the ensemble, which govern target recognition and how these proteins function. In this work, we investigated the macromolecular crowding effects on the dynamics of several IDPs by measuring the NMR spin relaxation parameters of three disordered proteins (ProTα, TC1, and α-synuclein) with different extents of residual structures. To aid the interpretation of experimental results, we also performed an MD simulation of ProTα. Based on the MD analysis, a simple model to correlate the observed changes in relaxation rates to the alteration in protein motions under crowding conditions was proposed. Our results show that 1) IDPs remain at least partially disordered despite the presence of high concentration of other macromolecules, 2) the crowded environment has differential effects on the conformational propensity of distinct regions of an IDP, which may lead to selective stabilization of certain target-binding motifs, and 3) the segmental motions of IDPs on the nanosecond timescale are retained under crowded conditions. These findings strongly suggest that IDPs function as dynamic structural ensembles in cellular environments.
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18
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Abstract
A living cell is a complex system that contains many biological macromolecules and small molecules necessary for survival, in a relatively small volume. It is within this crowded and complex cellular environment that proteins function making in-cell studies of protein structure and binding interactions an exciting and important area of study. Nuclear magnetic resonance (NMR) spectroscopy is a particularly attractive method for in-cell studies of proteins since it provides atomic-level data noninvasively in solution. In addition, NMR has recently undergone significant advances in instrumentation to increase sensitivity and in methods development to reduce data acquisition times for multidimensional experiments. Thus, NMR spectroscopy lends itself to studying proteins within a living cell, and recently "in-cell NMR" studies have been reported from several laboratories. To date, this technique has been successfully applied in Escherichia coli (E. coli), Xenopus laevis (X. laevis) oocytes, and HeLa host cells. Demonstrated applications include protein assignment as well as de novo 3D protein structure determination. The most common use, however, is to probe binding interactions and structural modifications directly from proton nitrogen correlation spectra. E. coli is the most extensively used cell type thus far and this chapter is largely confined to reviewing recent literature and describing methods and detailed protocols for in-cell NMR studies in this bacterial cell.
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Bertini I, Felli IC, Gonnelli L, Kumar M V V, Pierattelli R. 13C direct-detection biomolecular NMR spectroscopy in living cells. Angew Chem Int Ed Engl 2011; 50:2339-41. [PMID: 21351349 DOI: 10.1002/anie.201006636] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Indexed: 11/09/2022]
Affiliation(s)
- Ivano Bertini
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
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Bertini I, Felli IC, Gonnelli L, Kumar M. V, Pierattelli R. 13C Direct-Detection Biomolecular NMR Spectroscopy in Living Cells. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006636] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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21
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Hänsel R, Foldynová-Trantírková S, Löhr F, Buck J, Bongartz E, Bamberg E, Schwalbe H, Dötsch V, Trantírek L. Evaluation of parameters critical for observing nucleic acids inside living Xenopus laevis oocytes by in-cell NMR spectroscopy. J Am Chem Soc 2010; 131:15761-8. [PMID: 19824671 DOI: 10.1021/ja9052027] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In-cell NMR spectroscopy of proteins in different cellular environments is a well-established technique that, however, has not been applied to nucleic acids so far. Here, we show that isotopically labeled DNA and RNA can be observed inside the eukaryotic environment of Xenopus laevis oocytes by in-cell NMR spectroscopy. One limiting factor for the observation of nucleic acids in Xenopus oocytes is their reduced stability. We demonstrate that chemical modification of DNA and RNA can protect them from degradation and can significantly enhance their lifetime. Finally, we show that the imino region of the NMR spectrum is devoid of any oocyte background signals enabling the detection even of isotopically nonlabeled molecules.
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Affiliation(s)
- Robert Hänsel
- Institute of Biophysical Chemistry, Goethe-University, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany
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22
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Liu S, Kokot S, Will G. Photochemistry and chemometrics—An overview. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2009. [DOI: 10.1016/j.jphotochemrev.2010.01.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Abstract
Atomic level characterization of proteins and other macromolecules in the living cell is challenging. Recent advances in NMR instrumentation and methods, however, have enabled in-cell studies with prospects for multidimensional spectral characterization of individual macromolecular components. We present NMR data on the in-cell behavior of the MetJ repressor from Escherichia coli, a protein that regulates the expression of genes involved in methionine biosynthesis. NMR studies of whole cells along with corresponding studies in cell lysates and in vitro preparations of the pure protein give clear evidence for extensive nonspecific interactions with genomic DNA. These interactions can provide an efficient mechanism for searching out target sequences by reducing the dependence on 3-dimensional diffusion through the crowded cellular environment. DNA provides the track for MetJ to negotiate the obstacles inherent in cells and facilitates locating and binding specific repression sites, allowing for timely control of methionine biosynthesis.
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24
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Sakakibara D, Sasaki A, Ikeya T, Hamatsu J, Hanashima T, Mishima M, Yoshimasu M, Hayashi N, Mikawa T, Wälchli M, Smith BO, Shirakawa M, Güntert P, Ito Y. Protein structure determination in living cells by in-cell NMR spectroscopy. Nature 2009; 458:102-5. [PMID: 19262674 DOI: 10.1038/nature07814] [Citation(s) in RCA: 258] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 01/22/2009] [Indexed: 11/09/2022]
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25
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Dötsch V. Investigation of proteins in living bacteria with in-cell NMR experiments. Top Curr Chem (Cham) 2008; 273:203-14. [PMID: 23605464 DOI: 10.1007/128_2007_21] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
In recent years NMR methods have been developed that enable the observation of proteins insideliving bacterial cells. Because of the sensitivity of the chemical shift to environmental changesthese in-cell NMR experiments can be used to study protein conformation, molecular interaction ordynamics in a protein's natural surrounding. Detection of proteins in the bacterial cytoplasmrelies on labeling of the protein of interest with NMR active isotopes. This review describes differentlabeling techniques based on either uniform (15)N or (13)Clabeling as well as amino acid specific labeling schemes. In addition potential applications of thesein-cell NMR experiments and their limitations are discussed.
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Affiliation(s)
- Volker Dötsch
- Institute of Biophysical Chemistry, University of Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany,
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26
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Selenko P, Wagner G. Looking into live cells with in-cell NMR spectroscopy. J Struct Biol 2007; 158:244-53. [PMID: 17502240 DOI: 10.1016/j.jsb.2007.04.001] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Revised: 04/02/2007] [Accepted: 04/03/2007] [Indexed: 11/23/2022]
Abstract
In-cell NMR spectroscopy has gained recent popularity since it provides means to analyze the conformational and functional properties of proteins inside living cells and at atomic resolution. High-resolution in-cell NMR spectroscopy was originally established in bacterial cells and based on a rationale that relies on protein over-expression and sample analysis within the same cellular environment. Here, we review in-cell NMR approaches in Xenopus laevis oocytes and evaluate potential future applications in other eukaryotic cell types.
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Affiliation(s)
- Philipp Selenko
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology (BCMP), Boston, MA 02115, USA.
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27
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Sakai T, Tochio H, Tenno T, Ito Y, Kokubo T, Hiroaki H, Shirakawa M. In-cell NMR spectroscopy of proteins inside Xenopus laevis oocytes. JOURNAL OF BIOMOLECULAR NMR 2006; 36:179-88. [PMID: 17031531 DOI: 10.1007/s10858-006-9079-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Accepted: 08/14/2006] [Indexed: 05/12/2023]
Abstract
In-cell NMR is an application of solution NMR that enables the investigation of protein conformations inside living cells. We have measured in-cell NMR spectra in oocytes from the African clawed frog Xenopus laevis. (15)N-labeled ubiquitin, its derivatives and calmodulin were injected into Xenopus oocytes and two-dimensional (1)H-(15)N correlation spectra of the proteins were obtained. While the spectrum of wild-type ubiquitin in oocytes had rather fewer cross-peaks compared to its in vitro spectrum, ubiquitin derivatives that are presumably unable to bind to ubiquitin-interacting proteins gave a markedly larger number of cross-peaks. This observation suggests that protein-protein interactions between ubiquitin and ubiquitin-interacting proteins may cause NMR signal broadening, and hence spoil the quality of the in-cell HSQC spectra. In addition, we observed the maturation of ubiquitin precursor derivative in living oocytes using the in-cell NMR technique. This process was partly inhibited by pre-addition of ubiquitin aldehyde, a specific inhibitor for ubiquitin C-terminal hydrolase (UCH). Our work demonstrates the potential usefulness of in-cell NMR with Xenopus oocytes for the investigation of protein conformations and functions under intracellular environmental conditions.
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Affiliation(s)
- Tomomi Sakai
- International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, 230-0045, Japan
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28
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Selenko P, Serber Z, Gadea B, Ruderman J, Wagner G. Quantitative NMR analysis of the protein G B1 domain in Xenopus laevis egg extracts and intact oocytes. Proc Natl Acad Sci U S A 2006; 103:11904-9. [PMID: 16873549 PMCID: PMC1523310 DOI: 10.1073/pnas.0604667103] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We introduce a eukaryotic cellular system, the Xenopus laevis oocyte, for in-cell NMR analyses of biomolecules at high resolution and delineate the experimental reference conditions for successful implementations of in vivo NMR measurements in this cell type. This approach enables quantitative NMR experiments at defined intracellular concentrations of exogenous proteins, which is exemplified by the description of in-cell NMR properties of the protein G B1 domain (GB1). Additional experiments in Xenopus egg extracts and artificially crowded in vitro solutions suggest that for this biologically inert protein domain, intracellular viscosity and macromolecular crowding dictate its in vivo behavior. These contributions appear particularly pronounced for protein regions with high degrees of internal mobility in the pure state. We also evaluate the experimental limitations of this method and discuss potential applications toward the in situ structural characterization of eukaryotic cellular activities.
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Affiliation(s)
- Philipp Selenko
- Departments of *Biological Chemistry and Molecular Pharmacology and
- To whom correspondence may be addressed. E-mail:
, , or
| | - Zach Serber
- Department of Molecular Pharmacology, Stanford University Medical School, 269 West Campus Drive, Stanford, CA 94305
| | - Bedrick Gadea
- Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115; and
| | - Joan Ruderman
- Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115; and
- To whom correspondence may be addressed. E-mail:
, , or
| | - Gerhard Wagner
- Departments of *Biological Chemistry and Molecular Pharmacology and
- To whom correspondence may be addressed. E-mail:
, , or
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29
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Szyperski T, Atreya HS. Principles and applications of GFT projection NMR spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44 Spec No:S51-60. [PMID: 16826541 DOI: 10.1002/mrc.1817] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The two defining features of G-matrix Fourier transform (GFT) projection NMR spectroscopy are (i) repeated joint sampling of several indirect chemical shift evolution periods of a multidimensional NMR experiment so that transfer amplitudes are generated which are proportional to all possible permutations of cosine and sine modulations of the individual shifts, and (ii) linear combination of the subspectra resulting from such repeated joint sampling in the time or frequency domain which yields edited subspectra containing signals encoding phase-sensitively detected linear combinations of the jointly sampled shifts. This review sketches the underlying principles of GFT NMR and outlines its relation to further developments such as the reconstruction of multidimensional NMR spectra.
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Affiliation(s)
- Thomas Szyperski
- Department of Chemistry, The State University of New York at Buffalo, The Northeast Structural Genomics Consortium, Buffalo, NY 14260, USA.
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30
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Coggins BE, Zhou P. PR-CALC: a program for the reconstruction of NMR spectra from projections. JOURNAL OF BIOMOLECULAR NMR 2006; 34:179-95. [PMID: 16604426 PMCID: PMC3635542 DOI: 10.1007/s10858-006-0020-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2005] [Accepted: 01/23/2006] [Indexed: 05/08/2023]
Abstract
Projection-reconstruction NMR (PR-NMR) has attracted growing attention as a method for collecting multidimensional NMR data rapidly. The PR-NMR procedure involves measuring lower-dimensional projections of a higher-dimensional spectrum, which are then used for the mathematical reconstruction of the full spectrum. We describe here the program PR-CALC, for the reconstruction of NMR spectra from projection data. This program implements a number of reconstruction algorithms, highly optimized to achieve maximal performance, and manages the reconstruction process automatically, producing either full spectra or subsets, such as regions or slices, as requested. The ability to obtain subsets allows large spectra to be analyzed by reconstructing and examining only those subsets containing peaks, offering considerable savings in processing time and storage space. PR-CALC is straightforward to use, and integrates directly into the conventional pipeline for data processing and analysis. It was written in standard C+ + and should run on any platform. The organization is flexible, and permits easy extension of capabilities, as well as reuse in new software. PR-CALC should facilitate the widespread utilization of PR-NMR in biomedical research.
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Affiliation(s)
- Brian E Coggins
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.
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